Alignments for a candidate for uxuA in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Salinicoccus carnicancri Crm

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_017549842.1 C792_RS0112735 mannonate dehydratase

Query= metacyc::MONOMER-17955
         (360 letters)



>NCBI__GCF_000330705.1:WP_017549842.1
          Length = 357

 Score =  421 bits (1083), Expect = e-122
 Identities = 198/358 (55%), Positives = 266/358 (74%), Gaps = 4/358 (1%)

Query: 1   MKLVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLK 60
           M + FRWYGE +D+VTL+QI+QIPGVEGVV AL     GEVWP EE+M++K+  +  G  
Sbjct: 1   MHMTFRWYGEGNDSVTLDQIKQIPGVEGVVWALHHRQAGEVWPEEEVMEVKKQADAHGFH 60

Query: 61  LEVIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKK 120
           L+V+ES+NVHEDIKLG  +RD YIENYK ++RN+AKAG +VVC+NFMPVFDW RTDL K+
Sbjct: 61  LDVVESINVHEDIKLGKASRDEYIENYKISLRNVAKAGARVVCFNFMPVFDWTRTDLFKE 120

Query: 121 LPDGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWDRLEKLRETFELYKNVDEE 180
           L DGS  + Y+   +E + PDELIK+  +   G+ +PGWE +RL+ + ++F+ Y+ VDEE
Sbjct: 121 LGDGSTALFYEKSKVENMDPDELIKQTTD--SGYTMPGWEPERLKTIEDSFKAYETVDEE 178

Query: 181 KLFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYN 240
           +L++N+ +FL  V+PV EE  +K+AIHPDDPPWS+F LPRII ++  IER L   DSP +
Sbjct: 179 QLWKNMEHFLLEVLPVAEEEGIKMAIHPDDPPWSVFNLPRIINSESAIERYLSISDSPSH 238

Query: 241 GITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDL 300
            +T C GSLGANPEN+IP +IR F    RI FAH+RN+K      F ET+H S  GS  +
Sbjct: 239 CLTLCSGSLGANPENDIPHIIRRFA--DRIAFAHIRNVKTYDNGDFIETSHRSRDGSVPI 296

Query: 301 FEVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDKMKKR 358
            +V++A+H+ G++GY+RPDHGR +W E  RPGYGLYDRALG  Y+ GLW+A +  K++
Sbjct: 297 DDVVRAYHEAGFKGYVRPDHGRHLWDEDCRPGYGLYDRALGIMYLWGLWDAYELEKRK 354


Lambda     K      H
   0.322    0.142    0.448 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 487
Number of extensions: 31
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 360
Length of database: 357
Length adjustment: 29
Effective length of query: 331
Effective length of database: 328
Effective search space:   108568
Effective search space used:   108568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_017549842.1 C792_RS0112735 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00695.hmm
# target sequence database:        /tmp/gapView.1293811.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-136  440.8   0.0    1.7e-75  240.5   0.0    2.0  2  NCBI__GCF_000330705.1:WP_017549842.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017549842.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.1   0.2   3.1e-63   3.1e-63       1     147 [.       1     149 [.       1     154 [. 0.95
   2 !  240.5   0.0   1.7e-75   1.7e-75     168     388 ..     141     349 ..     137     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 3.1e-63
                             TIGR00695   1 meqtfrwyGr.ndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheei 71 
                                           m++tfrwyG+ nd+v+l++++q+ G++G+v+alhh+  Gevw  ee+ + k++ +  G++ +vves++vhe+i
  NCBI__GCF_000330705.1:WP_017549842.1   1 MHMTFRWYGEgNDSVTLDQIKQIpGVEGVVWALHHRQAGEVWPEEEVMEVKKQADAHGFHLDVVESINVHEDI 73 
                                           89*********************************************************************** PP

                             TIGR00695  72 klqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrp 144
                                           kl++  +++yienyk +lrn+a+ G +vvc+nfmpv+dwtrtdl++el dGs+al+++k kv+ ++   l + 
  NCBI__GCF_000330705.1:WP_017549842.1  74 KLGKASRDEYIENYKISLRNVAKAGARVVCFNFMPVFDWTRTDLFKELGDGSTALFYEKSKVENMDPDELIKQ 146
                                           ****************************************************************997655555 PP

                             TIGR00695 145 dae 147
                                            ++
  NCBI__GCF_000330705.1:WP_017549842.1 147 TTD 149
                                           455 PP

  == domain 2  score: 240.5 bits;  conditional E-value: 1.7e-75
                             TIGR00695 168 edkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprp 240
                                           ++  + t +    +pG+e+ e+l+ i++ ++ay ++dee+l++n+  fl e+lpvaee G+kmaihpddpp+ 
  NCBI__GCF_000330705.1:WP_017549842.1 141 DELIKQTTDSGYTMPGWEP-ERLKTIEDSFKAYETVDEEQLWKNMEHFLLEVLPVAEEEGIKMAIHPDDPPWS 212
                                           55556666667789*****.***************************************************** PP

                             TIGR00695 241 ilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkreenpktfhe 313
                                           ++ lpri+ ++  +++   isdsp+ ++tlc+Gs+G++++nd+ +++++fadri fah+r+vk ++n+ +f+e
  NCBI__GCF_000330705.1:WP_017549842.1 213 VFNLPRIINSESAIERYLSISDSPSHCLTLCSGSLGANPENDIPHIIRRFADRIAFAHIRNVKTYDNG-DFIE 284
                                           ********************************************************************.**** PP

                             TIGR00695 314 aahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlela 386
                                           ++h ++d+++   +  v+   h    +G    + vrpdhGr+l+d   + ++pGy++++r++G+++l Gl++a
  NCBI__GCF_000330705.1:WP_017549842.1 285 TSHRSRDGSVP--IDDVVRAYHEAGFKG----Y-VRPDHGRHLWD---EDCRPGYGLYDRALGIMYLWGLWDA 347
                                           **********9..9*********9999*....7.9**********...9************************ PP

                             TIGR00695 387 lk 388
                                           ++
  NCBI__GCF_000330705.1:WP_017549842.1 348 YE 349
                                           98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (357 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.15
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources